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  • 1. Barboutis, Christos
    et al.
    Henshaw, Ian
    Stockholm University, Faculty of Science, Department of Zoology.
    Kullberg, Cecilia
    Stockholm University, Faculty of Science, Department of Zoology.
    Nikolopoulou, Stamatina
    Fransson, Thord
    Fuelling in front of the barrier-are there age based behavioral differences in Garden Warblers Sylvia borin?2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, article id e319Article in journal (Refereed)
    Abstract [en]

    Garden Warblers Sylvia borin were studied during autumn stopover in Crete before crossing the barrier of the Mediterranean Sea and the Sahara Desert. Birds followed with transmitters show extensive stopover periods, which were longer in first-year birds, 16 days, compared with adult birds, 14 days. The distribution of body masses from birds trapped in fig trees were used to estimate the departure body mass and the results found indicate that both age categories on average depart with a fuel load close to 100% of lean body mass. The movement of transmitter birds shows differences between first-year and adult birds. Adult birds move further away from the release site and many also left the study area. Several were found settled outside the study area, up to 17 km away, indicating that they regularly make longer stopover movements. It is suggested that this might be a result of that they return to a place where they stayed during an earlier migration. It was shown that stopover site fidelity exists and nine garden warblers were recaptured in the area during a following autumn. The results found highlights the importance of stopover areas close to the Sahara Desert.

  • 2. Belton, Lydia E.
    et al.
    Cameron, Elissa Z.
    Dalerum, Fredrik
    Stockholm University, Faculty of Science, Department of Zoology. University of Pretoria, South Africa; University of Oviedo, Spa.
    Spotted hyaena space use in relation to human infrastructure inside a protected area2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e2596Article in journal (Refereed)
    Abstract [en]

    Increasing human population growth has led to elevated levels of human-carnivore conflict. However, some carnivore populations have adapted to urban environments and the resources they supply. Such associations may influence carnivore ecology, behaviour and life-history. Pockets of urbanisation sometimes occur within protected areas, so that anthropogenic influences on carnivore biology are not necessarily confined to unprotected areas. In this study we evaluated associations between human infrastructure and related activity and space use of spotted hyaenas within one of the largest protected areas in South Africa, the Kruger National Park. Home range size was smaller for the dominant female of a clan living in close proximity to humans than that of the dominant female of a clan without direct access to human infrastructure. The home range including human infrastructure was also used less evenly during the night, presumably when the animals were active. Within this home range, a village area was preferred during the night, when the least modified areas within the village were preferred and administration and highly modified areas were avoided. During the day, however, there were no preference or avoidance of the village area, but all habitats except unmodified habitats within the village area were avoided. We suggest that human infrastructure and associated activity influenced hyaena space use, primarily through alterations in the spatial distribution of food. However, these effects may have been indirectly caused by habitat modification that generated favourable hunting habitat rather than a direct effect caused by access to human food such as garbage. Because of the often pivotal effects of apex predators in terrestrial ecosystems, we encourage further work aimed to quantify how human presence influences large carnivores and associated ecosystem processes within protected areas.

  • 3.
    Campennì, Marco
    et al.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre.
    Schino, Gabriele
    Symmetry-based reciprocity: evolutionary constraints on a proximate mechanism2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id e1812Article in journal (Refereed)
    Abstract [en]

    Background. While the evolution of reciprocal cooperation has attracted an enormous attention, the proximate mechanisms underlying the ability of animals to cooperate reciprocally are comparatively neglected. Symmetry-based reciprocity is a hypothetical proximate mechanism that has been suggested to be widespread among cognitively unsophisticated animals. Methods. We developed two agent-baseds model of symmetry-based reciprocity (one relying on an arbitrary tag and the other on interindividual proximity) and tested their ability both to reproduce significant emergent features of cooperation in group living animals and to promote the evolution of cooperation. Results. Populations formed by', agents adopting symmetry-based reciprocity showed differentiated social relationships and a positive correlation between cooperation given and received: two common aspects of animal cooperation. However, when reproduction and selection across multiple generations were added to the models, agents adopting symmetry-based reciprocity were outcompeted by selfish agents that never cooperated. Discussion. In order to evolve, hypothetical proximate mechanisms must be able to from stand competition alternative strategies. While the results of our simulations require confirmation using analytical methods, we provisionally suggest symmetry based reciprocity is to be abandoned as a possible proximate mechanism underlying the ability of animals to reciprocate cooperative interactions.

  • 4. Dhaygude, Kishor
    et al.
    Trontti, Kalevi
    Paviala, Jenni
    Morandin, Claire
    Wheat, Christopher
    Stockholm University, Faculty of Science, Department of Zoology.
    Sundström, Liselotte
    Helanterä, Heikki
    Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3998Article in journal (Refereed)
    Abstract [en]

    Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.

  • 5. Didion, John P.
    et al.
    Martin, Marcel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Collins, Francis S.
    Atropos: specific, sensitive, and speedy trimming of sequencing reads2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3720Article in journal (Refereed)
    Abstract [en]

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leadingedge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github. com/jdidion/atropos.

  • 6. Eich, Andreas
    et al.
    Ford, Amanda K.
    Stockholm University, Faculty of Science, Stockholm Resilience Centre. Leibniz Centre for Tropical Marine Research (ZMT), Germany; University of Bremen, Germany.
    Nugues, Maggy M.
    McAndrews, Ryan S.
    Wild, Christian
    Ferse, Sebastian C. A.
    Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6380Article in journal (Refereed)
    Abstract [en]

    Observations of coral-algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral-turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora-coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral-algal contacts.

  • 7.
    Eklöf, Johan
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Austin, Åsa
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Bergström, Ulf
    Donadi, Serena
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Eriksson, Britas D. H. K.
    Hansen, Joakim
    Stockholm University, Faculty of Science, Stockholm University Baltic Sea Centre.
    Sundblad, Göran
    Size matters: relationships between body size and body mass of common coastal, aquatic invertebrates in the Baltic Sea2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5Article in journal (Refereed)
    Abstract [en]

    Background. Organism biomass is one of the most important variables in ecological studies, making biomass estimations one of the most common laboratory tasks. Biomass of small macroinvertebrates is usually estimated as dry mass or ash-free dry mass (hereafter `DM' vs. 'AFDM') per sample; a laborious and time consuming process, that often can be speeded up using easily measured and reliable proxy variables like body size or wet (fresh) mass. Another common way of estimating AFDM (one of the most accurate but also time-consuming estimates of biologically active tissue mass) is the use of AFDM/DM ratios as conversion factors. So far, however, these ratios typically ignore the possibility that the relative mass of biologically active vs. non-active support tissue (e.g., protective exoskeleton or shell)-and therefore, also AFDM/DM ratios-may change with body size, as previously shown for taxa like spiders, vertebrates and trees. Methods. We collected aquatic, epibenthic macroinvertebrates (>1 mm) in 32 shallow bays along a 360 km stretch of the Swedish coast along the Baltic Sea; one of the largest brackish water bodies on Earth. We then estimated statistical relationships between the body size (length or height in mm), body dry mass and ash-free dry mass for 14 of the most common taxa; five gastropods, three bivalves, three crustaceans and three insect larvae. Finally, we statistically estimated the potential influence of body size on the AFDM/DM ratio per taxon. Results. For most taxa, non-linear regression models describing the power relationship between body size and (i)DM and (ii) AFDM fit the data well (as indicated by low SE and high R-2). Moreover, for more than half of the taxa studied (including the vast majority of the shelled molluscs), body size had a negative influence on organism AFDM/DM ratios. Discussion. The good fit of the modelled power relationships suggests that the constants reported here can be used to quickly estimate organism dry-and ash-free dry mass based on body size, thereby freeing up considerable work resources. However, the considerable differences in constants between taxa emphasize the need for tax on specific relationships, and the potential dangers associated with ignoring body size. The negative influence of body size on the AFDM/DM ratio found in a majority of the molluscs could be caused by increasingly thicker shells with organism age, and/or spawning-induced loss of biologically active tissue in adults. Consequently, future studies utilizing AFDM/DM (and presumably also AFDM/wet mass) ratios should carefully assess the potential influence of body size to ensure more reliable estimates of organism body mass.

  • 8. Garcia, Danilo
    et al.
    MacDonald, Shane
    Stockholm University, Faculty of Social Sciences, Department of Psychology. University of Gothenburg, Sweden; Örebro University, Sweden.
    Archer, Trevor
    Two different approaches to the affective profiles model: median splits (variable-oriented) and cluster analysis (person-oriented)2015In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 3, article id e1380Article in journal (Refereed)
    Abstract [en]

    Background. The notion of the affective system as being composed of two dimensions led Archer and colleagues to the development of the affective profiles model. The model consists of four different profiles based on combinations of individuals' experience of high/low positive and negative affect: self-fulfilling, low affective, high affective, and self-destructive. During the past 10 years, an increasing number of studies have used this person-centered model as the backdrop for the investigation of between and within individual differences in ill-being and well-being. The most common approach to this profiling is by dividing individuals' scores of self-reported affect using the median of the population as reference for high/low splits. However, scores just-above and just-below the median might become high and low by arbitrariness, not by reality. Thus, it is plausible to criticize the validity of this variable-oriented approach. Our aim was to compare the median splits approach with a person-oriented approach, namely, cluster analysis. Method. The participants (N = 2,225) were recruited through Amazons'Mechanical Turk and asked to self-report affect using the Positive Affect Negative Affect Schedule. We compared the profiles' homogeneity and Silhouette coefficients to discern differences in homogeneity and heterogeneity between approaches. We also conducted exact cell-wise analyses matching the profiles from both approaches and matching profiles and gender to investigate profiling agreement with respect to affectivity levels and affectivity and gender. All analyses were conducted using the ROPstat software. Results. The cluster approach (weighted average of cluster homogeneity coefficients = 0.62, Silhouette coefficients = 0.68) generated profiles with greater homogeneity and more distinctive from each other compared to the median splits approach (weighted average of cluster homogeneity coefficients = 0.75, Silhouette coefficients = 0.59). Most of the participants (n = 1,736, 78.0%) were allocated to the same profile (Rand Index =.83), however, 489 (21.98%) were allocated to different profiles depending on the approach. Both approaches allocated females and males similarly in three of the four profiles. Only the cluster analysis approach classified men significantly more often than chance to a self-fulfilling profile (type) and females less often than chance to this very same profile (antitype). Conclusions. Although the question whether one approach is more appropriate than the other is still without answer, the cluster method allocated individuals to profiles that are more in accordance with the conceptual basis of the model and also to expected gender differences. More importantly, regardless of the approach, our findings suggest that the model mirrors a complex and dynamic adaptive system.

  • 9.
    Ghirlanda, Stefano
    Stockholm University, Faculty of Humanities, Department of Archaeology and Classical Studies, Centre for the Study of Cultural Evolution. Brooklyn College, USA; CUNY Graduate Center, USA.
    Can squirrel monkeys learn an AB(n)A grammar? A re-evaluation of Ravignani et al. (2013)2017In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 5, article id e3806Article in journal (Refereed)
    Abstract [en]

    Ravignani et al (2013) abituated squirrel monkeys to sound sequences conforming to an ABnA grammar (n = 1, 2, 3), then tested them for their reactions to novel grammatical and non -grammatical sequences. Although they conclude that the monkeys consistently recognized and generalized the sequence AB(n)A, I remark that this conclusion is not robust. The statistical significance of results depends on specific choices of data analysis, namely dichotomization of the response variable and omission of specific data points. Additionally, there is little evidence of generalization to novel patterns (n = 4, 5), which is important to conclude that the monkeys recognized the AB(n)A grammar beyond the habituation patterns. Lastly, many test sequences were perceptually similar to habituation sequences, raising the possibility that the monkeys may have generalized based on perceptual similarity rather than based on grammaticality.

  • 10. Josephson, Henrik
    et al.
    Carlbring, Per
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Clinical psychology.
    Forsberg, Lars
    Rosendahl, Ingvar
    People with gambling disorder and risky alcohol habits benefit more from motivational interviewing than from cognitive behavioral group therapy2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id 1899Article in journal (Refereed)
    Abstract [en]

    Background. Effective psychological treatment, including cognitive behavioral therapy and motivational interviewing (MI), is available for people with problematic gambling behaviors. To advance the development of treatment for gambling disorder, it is critical to further investigate how comorbidity impacts different types of treatments. The purpose of this study was to investigate whether screening for risky alcohol habits can provide guidance on whether people with gambling disorder should be recommended cognitive behavioral group therapy (CBGT) or MI.

    Methods. The present study is a secondary analysis of a previous randomized controlled trial that compared the effects of CBGT, MI and a waitlist control group in the treatment of disordered gambling. Assessment and treatment was conducted at an outpatient dependency clinic in Stockholm, Sweden, where 53 trial participants with gambling disorder began treatment. A modified version of the National Opinion Research Centre DSM-IV Screen for gambling problems was used to assess gambling disorder. The Alcohol Use Disorders Identification Test (AUDIT) was used to screen for risky alcohol habits.

    Results. The interaction between treatment and alcohol habits was significant and suggests that patients with gambling disorder and risky alcohol habits were better helped by MI, while those without risky alcohol habits were better helped by CBGT.

    Conclusions. The results support a screening procedure including the AUDIT prior to starting treatment for gambling disorder because the result of the screening can provide guidance in the choice of treatment. Patients with gambling disorder and risky alcohol habits are likely to be best helped if they are referred to MI, while those without risky alcohol habits are likely to be best helped if they are referred to CBGT.

  • 11.
    Lindner, Philip
    et al.
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Clinical psychology. Karolinska Institute, Sweden.
    Carlbring, Per
    Stockholm University, Faculty of Social Sciences, Department of Psychology, Clinical psychology.
    Flodman, Erik
    Hebert, Amanda
    Poysti, Stephanie
    Hagkvist, Filip
    Johansson, Robert
    Zetterqvist Westin, Vendela
    Berger, Thomas
    Andersson, Gerhard
    Does cognitive flexibility predict treatment gains in Internet-delivered psychological treatment of social anxiety disorder, depression, or tinnitus?2016In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 4, article id E1934Article in journal (Refereed)
    Abstract [en]

    Little is known about the individual factors that predict outcomes in Internet-administered psychological treatments. We hypothesized that greater cognitive flexibility (i.e. the ability to simultaneously consider several concepts and tasks and switch effortlessly between them in response to changes in environmental contingencies) would provide a better foundation for learning and employing the cognitive restructuring techniques taught and exercised in therapy, leading to greater treatment gains. Participants in three trials featuring Internet-administered psychological treatments for depression (n = 36), social anxiety disorder (n = 115) and tinnitus (n = 53) completed the 64-card Wisconsin Card Sorting Test (WCST) prior to treatment. We found no significant associations between perseverative errors on the WCST and treatment gains in any group. We also found low accuracy in the classification of treatment responders. We conclude that lower cognitive flexibility, as captured by perseverative errors on the WCST, should not impede successful outcomes in Internet-delivered psychological treatments.

  • 12. Loderer, Christoph
    et al.
    Holmfeldt, Karin
    Lundin, Daniel
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Linnaeus University, Sweden.
    Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6700Article in journal (Refereed)
    Abstract [en]

    Ribonucleotide reductases (RNR) are essential enzymes for all known life forms. Their current taxonomic distribution suggests extensive horizontal gene transfer e.g., by processes involving viruses. To improve our understanding of the underlying processes, we characterized a monomeric class II RNR (NrdJm) enzyme from a Thermus virus, a subclass not present in any sequenced Thermus spp. genome. Phylogenetic analysis revealed a distant origin of the nrdJm gene with the most closely related sequences found in mesophiles or moderate thermophiles from the Firmicutes phylum. GC-content, codon usage and the ratio of coding to non-coding substitutions (dN/dS) suggest extensive adaptation of the gene in the virus in terms of nucleotide composition and amino acid sequence. The NrdJm enzyme is a monomeric B-12-dependent RNR with nucleoside triphosphate specificity. It exhibits a temperature optimum at 60-70 degrees C, which is in the range of the growth optimum of Thermus spp. Experiments in combination with the Thermus thermophilus thioredoxin system show that the enzyme is able to retrieve electrons from the host NADPH pool via host thioredoxin and thioredoxin reductases. This is different from other characterized viral RNRs such as T4 phage RNR, where a viral thioredoxin is present. We hence show that the monomeric class II RNR, present in Thermus viruses, was likely transferred from an organism phylogenetically distant from the one they were isolated from, and adapted to the new host in genetic signature and amino acids sequence.

  • 13. Matos-Maravi, Pável
    et al.
    Ritter, Camila Duarte
    Barnes, Christopher J.
    Nielsen, Martin
    Olsson, Urban
    Wahlberg, Niklas
    Marquina, Daniel
    Stockholm University, Faculty of Science, Department of Zoology. Swedish Museum of Natural History, Sweden.
    Sääksjärvi, Ilari
    Antonelli, Alexandre
    Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies2019In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 7, article id e6727Article in journal (Refereed)
    Abstract [en]

    Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.

  • 14. Mousavi, Fariba
    et al.
    Garcia, Danilo
    Jimmefors, Alexander
    Archer, Trevor
    Ewalds-Kvist, Béatrice
    Stockholm University, Faculty of Social Sciences, Department of Psychology. University of Turku, Finland.
    Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, p. e410-Article in journal (Refereed)
    Abstract [en]

    Background. Illicit drug use influences people’s lives and elicits unwanted behaviour. Current research shows that there is an increase in young people’s drug use in Sweden. The aim was to investigate Swedish high-school pupils’ attitudes, impulsiveness and gender differences linked to drug use. Risk and protective factors relative to drug use were also a focus of interest.

    Method. High school pupils (n = 146) aged 17–21 years, responded to the Adolescent Health and Development Inventory, Barratt Impulsiveness Scale and Knowledge, and the Attitudes and Beliefs. Direct logistic, multiple regression analyses, and Multivariate Analysis of Variance were used to analyze the data.

    Results. Positive Attitudes towards drugs were predicted by risk factors (odds ratio = 37.31) and gender (odds ratio = .32). Risk factors (odds ratio = 46.89), positive attitudes towards drugs (odds ratio = 4.63), and impulsiveness (odds ratio = 1.11) predicted drug usage. Risk factors dimensions Family, Friends and Individual Characteristic were positively related to impulsiveness among drug users. Moreover, although boys reported using drugs to a greater extent, girls expressed more positive attitude towards drugs and even reported more impulsiveness than boys.

    Conclusion. This study reinforces the notion that research ought to focus on gender differences relative to pro-drug attitudes along with testing for differences in the predictors of girls’ and boys’ delinquency and impulsiveness. Positive attitudes towards drugs among adolescents seem to be part of a vicious circle including risk factors, such as friendly drug environments (e.g., friends who use drugs) and unsupportive family environments, individual characteristics, and impulsiveness.

  • 15.
    Näslund, Joacim
    et al.
    Stockholm University, Faculty of Science, Department of Zoology.
    Lundgren, Markus
    Mapping the distribution of scale-rayed wrasse Acantholabrus palloni in Swedish Skagerrak using angling records2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e5900Article in journal (Refereed)
    Abstract [en]

    In this paper, we map the distribution of scale-rayed wrasse Acantholubrus palloni in eastern Skagerrak based on a combination of verified and personally communicated angling records. Long thought to be occasional vagrants outside its known range in the eastern Atlantic Ocean and Mediterranean Sea, we ask if this rare and understudied labrid has expanded its range and become established in Swedish waters. A recent surge in verified angling records in the Swedish Anglers Association's specimen database Storfiskregistret provides information to suggest that this species should no longer be considered an occasional guest, but rather a species established in the Swedish parts of Skagerrak. These records are supported by additional personal communications with anglers. The species is currently well spread geographically along the Swedish Skagerrak coast, with many locations providing repeated captures of adult fish over multiple years. The typical Swedish catch sites are rocky reefs located between the general 40- and 80-m depth curves, likely influenced by currents bringing higher-salinity water from the North Sea. The present study show that angling records can provide an important, but underutilized, resource for mapping the distribution of data-deficient fish species.

  • 16.
    van der Bijl, Wouter
    Stockholm University, Faculty of Science, Department of Zoology.
    phylopath: Easy phylogenetic path analysis in R2018In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 6, article id e4718Article in journal (Refereed)
    Abstract [en]

    Confirmatory path analysis allows researchers to evaluate and compare causal models using observational data. This tool has great value for comparative biologists since they are often unable to gather experimental data on macro-evolutionary hypotheses, but is cumbersome and error-prone to perform. I introduce phylopath, an R package that implements phylogenetic path analysis (PPA) as described by von Hardenberg Gonzalez-Vayer (2113). In addition to the published method, I provide support for the inclusion of binary variables. I illustrate PPA and phylopath by recreating part of a study on the relationship between brain size and vulnerability to extinction. The package aims to make the analysis straight-forward, providing convenience functions, and several plotting methods, which I hope will encourage the spread of the method.

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